Re: [galaxy-dev] Error on database_connection statement in universe_wsgi.ini file
Hi Don't use the '' and ''. That was just a sign to signal where to insert what. Have you also looked at James' reply? Regards, Hans On 08/08/2012 01:51 AM, Kenneth Auerbach wrote: Hi, Now I'm using this database_connection in my universe_wsgi.ini file: database_connection = mysql://username:password@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock and I still get this: - linuxmint galaxy-galaxy-dist-ec29ce8e27a1 # sh run.sh Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 276, in command relative_to=base, global_conf=vars) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 313, in loadapp **kw) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 224, in loadobj global_conf=global_conf) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 248, in loadcontext global_conf=global_conf) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 413, in get_context section) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 458, in _context_from_explicit value = import_string(found_expr) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 18, in import_string return pkg_resources.EntryPoint.parse(x=+s).load(False) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/lib/pkg_resources.py, line 1997, in parse src ValueError: (EntryPoint must be in 'name=module:attrs [extras]' format, 'x=galaxy.web.buildapp:app_factory\ndatabase_connection = mysql://wolf:flewald@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock') - Any idea what the problem could be? Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Workflows do not open anymore
Hello, after commit 29680fa5c35e we are not able to open workflows anymore. The error message is: TypeError: mako.template.Template object at 0x6dc8e10 is not JSON serializable And the problematic changeset is here: https://bitbucket.org/galaxy/galaxy-central/changeset/29680fa5c35e6c22a6b7208015237b95d4bce2cc#chg-lib/galaxy/tools/__init__.py Hope that helps, Bjoern -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy and Toolshed issues
Hi Greg. I had the tool shed and Galaxy opened in two tabs so this may have been the issue. I am using a mysql database. I will check tis again when I next update Galaxy and let you know if there is a problem. Thanks for your help Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 1 Aug 2012 11:24:44 -0400: Hi Shaun, Thanks very much for the details - they have helped me discover a weakness which I've fixed. if the browser page is opened to the Manage repository page in the tool shed when the repository is cloned for the first time, the repository name could be changed after the clone. This has been fixed in change set 7441:513a95abb738. However, your step 4 (return to toolshed, find repository) implies that this is not what you were doing. Can you update to the tip from Galaxy central and see if my latest fix still allows you to change the repository name after it has been cloned in your environment? If so, I'll need to figure out what you are doing differently that is still allowing for this. Also, what database are you using? I found some issues with sqlite that I've fixed that would not eve have allowed for the repository to be cloned in the first place. Thanks again! Greg On Aug 1, 2012, at 7:03 AM, SHAUN WEBB wrote: Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 1 Aug 2012 06:23:11 -0400: I cannot reproduce this behavior, so can you let me know the steps you use to do so? I need the page on which you are able to change the name of the tool shed repository in the tool shed after it has been cloned. 1. Create new repository in local toolshed and fill in name, synopsis, description and category 2. Upload a .pl script file then upload a .xml wrapper file 3. Go to my local Galaxy and install repository via admin panel 4. Return to toolshed, find repository and name etc are still editable Screen shot attached. I noticed that times downloaded is still 0 after installing the repository. I have cloned the repository using hg on command line and this is still not updated. I'm guessing this is the problem. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] FTP upload - symlink to uploaded data
Dear devs, Question about FTP upload: is it correct that Galaxy copies the data from the FTP upload directory to galaxy database instead of symlinking? Can I set somewhere the option to symlink instead of copying? I run galaxy in a small virtual machine. The Galaxy database is on a network share. With 'get data' - 'Upload file', when importing the files I have uploaded with FTP, there is a process filling up the /tmp directory with the file I want to import. Kind regards, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Changing Install Directory
Hi all, I would like to change the name of the directory where my Galaxy instance is installed. What is the best way to go about this without breaking any paths/links. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Changing Install Directory
Hi Shaun, the main directory name can be arbitrary i think, if you are referring to galaxy-dist or galaxy-central. Maybe check the config files especially community_wsgi.ini if you have configured something special. If you are running galaxy behind a apache-proxy you have to adapt the rewrite rules. Cheerio, Bjoern Hi all, I would like to change the name of the directory where my Galaxy instance is installed. What is the best way to go about this without breaking any paths/links. Thanks Shaun -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] How to block anonymous access and disallow user registration
Re-Post to galaxy-dev On 8/6/12 11:59 AM, Joel Rosenberg wrote: Hello, I've just set up my own instance of Galaxy running in AWS and had a security question that I couldn't find an answer to on the wiki. I'd like to prevent people from hitting my public Amazon IP and using Galaxy. Is t! here a way to prevent anonymous users from accessing any part of Galaxy except a login prompt and have user registration be invite-only (or perhaps turn it off completely once a handful of accounts have been created)? Thanks, -Joel ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Starting a Cloud Instance
Re-Post to galaxy-dev On 8/7/12 3:01 AM, Mark Lindsay wrote: I wondered if you might be able to help. I have very little computing experience but have been trying to launch a cloud instance for the last 24 hrs. Initially I had problems launching the instance in Sahari i.e. it kept saying that it could not connect to the relevant page. When I have finally got top the CloudMan launch page it is giving the following message [Critical] Volume 'vol-dd6397db' is located in the wrong availability zone for this instance. You MUST terminate this instance and start a new one in zone 'us-east-1a' despite the fact that I am sure I have started in zone 'us-east-1a. How important are the security codes and keys? BW Mark ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Workflows do not open anymore
Fixed in 4d22e26e595a Thanks, J. On Aug 8, 2012, at 6:05 AM, Björn Grüning wrote: Hello, after commit 29680fa5c35e we are not able to open workflows anymore. The error message is: TypeError: mako.template.Template object at 0x6dc8e10 is not JSON serializable And the problematic changeset is here: https://bitbucket.org/galaxy/galaxy-central/changeset/29680fa5c35e6c22a6b7208015237b95d4bce2cc#chg-lib/galaxy/tools/__init__.py Hope that helps, Bjoern -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to block anonymous access and disallow user registration
Hi Jennifer, In universe.wsgi.ini, you can set the following parameters require_login = True -- no anonymous user can access your Galaxy allow_user_creation = False -- users can not register, only an admin can create an account for them (under admin/manage users). Tell me if you have other questions related to this matter Sincerely David Date: Wed, 8 Aug 2012 04:42:54 -0700 From: j...@bx.psu.edu To: thisisj...@hotmail.com; galaxy-...@bx.psu.edu Subject: [galaxy-dev] How to block anonymous access and disallow user registration Re-Post to galaxy-dev On 8/6/12 11:59 AM, Joel Rosenberg wrote: Hello, I've just set up my own instance of Galaxy running in AWS and had a security question that I couldn't find an answer to on the wiki. I'd like to prevent people from hitting my public Amazon IP and using Galaxy. Is t! here a way to prevent anonymous users from accessing any part of Galaxy except a login prompt and have user registration be invite-only (or perhaps turn it off completely once a handful of accounts have been created)? Thanks, -Joel ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] EBI SRA download: connection time out
Hi all, I do not succeed in downloading data from SRA. For every dataset I use (from smaller one to bigger ones) I get this error, after running for a few minutes. The remote data source application may be off line, please try again later. Error: [Errno ftp error] [Errno 110] Connection timed out Any idea? cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem with get data/uploading file
Hi David, We found while creating our VMs for the GCC Training Day that browsers within the VM (Ubuntu 12.04) were not able to consistently upload using the AJAX/Hidden iframe method that Galaxy uses by default. I'm investigating the problem. Are you able to upload using Firefox/Chrome/Safari on other OS's, or is the problem specific to Fedora? --nate On Aug 1, 2012, at 9:33 AM, David Roquis wrote: Hello again, I've read on the mailing list that some galaxy users are facing the same problem as I do, and that it seems to be related to the internet browser. Indeed, I noticed that I have no problem uploading data while using IE 8 or 9, but that it almost never works with Firefox, Chrome or Safari. I also noticed that when it doesn't work, the script upload.py is not launched at all. Could it be a javascript bug? Thanks again for possible help David From: david_roq...@hotmail.com To: galaxy-dev@lists.bx.psu.edu Date: Mon, 16 Jul 2012 09:50:34 -0400 Subject: [galaxy-dev] Problem with get data/uploading file Dear Galaxy community, I have a problem with uploading data on Galaxy, using the get data/upload file tool, and I can't figure out where the trouble comes from. Basically, when I try to upload files (size ranging from less than 1 Mo up to 600 Mo), sometimes it works, sometimes it doesn't (keep uploading forever), and I don't get any error message when it doesn't work. I can't find a pattern on when it works or not, it seems pretty random. It don't think it is related to the files I use, because I tried with different files, of different types and format, and the exact same file can sometimes be uploaded, sometimes not. One thing I have noticed is that when the upload is successful, a file is created in /tmp/, and when the upload runs forever, no new file appears in /tmp/. I have tried a couple of basic things to solve the problem: emptying the /tmp/, restarting galaxy, deleting permanently my history, etc. Sometimes I can upload 4-5 files in a row, then it stops working, and some other time I can't even upload one. When one upload keep running forever, even if I cancel it, no further uploads will work. I have to stop the uploads and restart galaxy, but it doesn't work 100% of the time (sometimes I have to try 2-3 times before I can upload again). I am facing this problem on two different instances of galaxy. A development one that I simply installed on my /home/ using mercurial and didn't modified at all, and a production one that I just set up following the Galaxy Team recommendations (using PostgreSQL and nginx with the upload module, and working on a dedicated Galaxy user account). I am a beginner in informatics, and since I get no error message, I don't know where to look for a way to solve this annoying problem. Uploading files using data libraries under the admin menu seems to be working perfectly all the time. Thank you very much for your help and advice. Sincerely David Roquis Ph.D. student University of Perpignan additional info: - I am using the latest version of galaxy, and my OS is Fedora 16 - I tried working with and without virtualenv (made no difference). - I don't know if this is related or not, but it seems quite strange to me. Whenever I try to access manage jobs in the admin section (on both instances), I get the following error message: This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs. How is that possible since I am not using multiple servers (especially for the development instance, which I haven't modified at all)? - debug = False is causing me a server error in the history frame (so I use True instead). ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] a problem with python version
On Aug 2, 2012, at 1:59 PM, Rui Wang wrote: Hi All, we are installing a local galaxy instance but we met something puzzling. we are running galaxy on cent os 5.x and python 2.6.1. when we tried to upload data, it failed with the message * Dataset generation errors Dataset 5: brain.fa Tool execution generated the following error message: /usr/usc/python/2.6.1/lib/python2.6/site-packages/pytz/tzinfo.py:5: DeprecationWarning: the sets module is deprecated from sets import Set * However, when we tried to use the galaxy version tied to the OS, which is 2.4.3, we were able to upload successfully. Did anyone have the same experience? Any advice will be greatly appreciated. Hi Rui, I'd suggest upgrading your version of pytz with `easy_install --upgrade pytz`. Newer versions should correctly handle importing sets. --nate Thanks, Rui ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] TopHat paired end
Hello, I am trying to do RNAseq analysis on Paired end data Illumina. I have about 4 files for each sample (2 forward and 2 reverse). I want to analyze the data in Galaxy. Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads for the sample. Ultimately, How do I run TopHat for paired-end data. When I select paired end data in Galaxy, it gives an option to upload both files should I upload both forward files once and reverse files once. Or should I combine both the files before running the TopHat. I am all confused. Any kind of help will be appreciated Thanks in advance ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] a problem with python version
Hi Nate, Thanks for the suggestion. Our cluster does not belong to us so we had to request that to be added by their sysadmin. Before that we modified the code in a few scripts to ignore the deprecation warning, that also fixed the problem, should we remove these mods now since the new pytz is installed? A separate question, do you happen to know where I could find the instructions for setting up job submission for PBS/torque? There are pieces and bits information here and there but I didn't see any comprehensive one... Best Regards, Rui On Wed, Aug 8, 2012 at 7:54 AM, Nate Coraor n...@bx.psu.edu wrote: On Aug 2, 2012, at 1:59 PM, Rui Wang wrote: Hi All, we are installing a local galaxy instance but we met something puzzling. we are running galaxy on cent os 5.x and python 2.6.1. when we tried to upload data, it failed with the message * Dataset generation errors Dataset 5: brain.fa Tool execution generated the following error message: /usr/usc/python/2.6.1/lib/python2.6/site-packages/pytz/tzinfo.py:5: DeprecationWarning: the sets module is deprecated from sets import Set * However, when we tried to use the galaxy version tied to the OS, which is 2.4.3, we were able to upload successfully. Did anyone have the same experience? Any advice will be greatly appreciated. Hi Rui, I'd suggest upgrading your version of pytz with `easy_install --upgrade pytz`. Newer versions should correctly handle importing sets. --nate Thanks, Rui ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] TopHat for paired end
Hello, I am trying to run TopHat for paired end and this is my first time using Galaxy and TopHat and I have a doubt regarding what to mention in Mean Inner Distance between Mate Pairs:The default value is 20. Should I leave the value or should I be changing the value. What is Mean Inner Distance between Mate Pairs:? Thanks ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Shell script to start Galaxy in multi-server environment
From: Nate Coraor [mailto:n...@bx.psu.edu] On Aug 2, 2012, at 2:56 PM, Karger, Amir wrote: We're upgrading to a late June Galaxy from a last-year Galaxy. We noticed that the docs say you no longer need 2 different .ini files. Great! Unfortunately, the multiprocess.sh in contrib/ still assumes you have multiple .ini files. multiprocess.sh is out of date, so I've removed it from galaxy-central. run.sh can start and stop all of your processes now, as described at: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application %20Scaling Thanks. Of course, reading some other people's posts and the wiki, it looks like it's not *required* to merge, just recommended. Which means our existing system of running the different scripts on different hosts should continue to work. We figure we can put off the merge thing for a bit. Meanwhile, we're able to restart, and get happy log messages from the jobrunner and two web servers (two servers running on different ports of a Tomcat host). And I can do an upload, which runs locally. But when I try to do a blast, which is supposed to submit to the cluster (and ran just fine on our old install), it hangs and never starts. I would think the database is working OK, since it shows me new history items when I upload and stuff. The web Galaxy log shows that I went to the tool page, and then has a ton of loads to root/history_item_updates, but nothing else. The job handler Galaxy log has nothing since the PID messages when the server started up most recently. A quick search of the archives didn't find anything obvious. (I don't have any obvious words to search for.) Any thoughts about where I should start looking to track this down? Thanks, -Amir ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Error on database_connection statement in universe_wsgi.ini file
On Aug 6, 2012, at 9:17 PM, Kenneth R. Auerbach wrote: Hello, Galaxy runs fine 'out of the box' with the default universe_wsgi.ini initialization file. But when I change the database_connection statement to connect to my MySql database, I get the errors below. Can you please tell what the problem is? Thanks! -Wolf. Modification to universe_wsgi.ini file: #database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE database_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock - Then when I type sh run.sh I get this: - wolf@linuxmint ~/Downloads/galaxy-galaxy-dist-ec29ce8e27a1 $ sh run.sh Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 276, in command relative_to=base, global_conf=vars) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 313, in loadapp **kw) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 224, in loadobj global_conf=global_conf) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 248, in loadcontext global_conf=global_conf) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 413, in get_context section) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 458, in _context_from_explicit value = import_string(found_expr) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 18, in import_string return pkg_resources.EntryPoint.parse(x=+s).load(False) File /home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/lib/pkg_resources.py, line 1997, in parse src ValueError: (EntryPoint must be in 'name=module:attrs [extras]' format, 'x=galaxy.web.buildapp:app_factory\ndatabase_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock') Hi Wolf, It looks like the 'paste.app_factory' option was somehow messed up. Can you double check that it looks like: paste.app_factory = galaxy.web.buildapp:app_factory And is the only 'paste.app_factory' entry in your config file? --nate ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Odd (possible latency/race?) problems post-upgrade
Hi,
Greg has just fixed this in 9f790bc90769. Thanks for letting us know!
--nate
On Aug 2, 2012, at 3:34 PM, Fields, Christopher J wrote:
I mentioned this on IRC, Nate indicated he was looking into it. My
short-term workaround was adding a 'sleep 9' in the process initiation loops
in 'run.sh' and 'run_multiple_processes.sh' (just after the python call) to
allow time between the start of each process.
chris
On Aug 2, 2012, at 7:46 AM, Jelle Scholtalbers j.scholtalb...@gmail.com
wrote:
Hi,
I'm experiencing the same problem after I configured the web
application scaling- although I have to say I still have the june 03
version from central. Has this been resolved in newer updates?
Cheers,
Jelle
On Mon, Jul 30, 2012 at 7:03 PM, Fields, Christopher J
cjfie...@illinois.edu wrote:
I'm seeing a possible latency issue or race condition when starting Galaxy
after the latest hg upgrade (July 20) from galaxy-dist; the prior upgrade
doesn't have this problem. We have small setup with one job manager/runner
and two web front-ends for testing load balancing:
…from universe_wsgi.ini:
--
[server:web0]
use = egg:Paste#http
port = 8080
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 7
[server:web1]
use = egg:Paste#http
port = 8081
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 7
[server:manager]
use = egg:Paste#http
port = 8079
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
--
If I run:
GALAXY_RUN_ALL=1 sh run.sh --daemon
I will intermittently see the following in the paster log for any of the
above services (example below is web1, but I have seen this for manager and
web0 as well). The traceback and error is the same in all cases ('File
exists: /home/a-m/galaxy/dist-database/tmp/work_tmp'):
--
galaxy.tool_shed.tool_shed_registry DEBUG 2012-07-30 11:40:10,194 Loading
references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2012-07-30 11:40:10,194 Loaded
reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-07-30 11:40:10,194 Loaded
reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2012-07-30 11:40:10,650 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-07-30 11:40:10,845 At database version
103
galaxy.tool_shed.migrate.check DEBUG 2012-07-30 11:40:10,940 psycopg2 egg
successfully loaded for postgres dialect
galaxy.tool_shed.migrate.check INFO 2012-07-30 11:40:10,986 At
migrate_tools version 3
galaxy.model.custom_types DEBUG 2012-07-30 11:40:10,994 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File /home/a-m/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 82, in
app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /home/a-m/galaxy/galaxy-dist/lib/galaxy/app.py, line 66, in __init__
self.installed_repository_manager.load_proprietary_datatypes()
File /home/a-m/galaxy/galaxy-dist/lib/galaxy/tool_shed/__init__.py, line
47, in load_proprietary_datatypes
installed_repository_dict =
galaxy.util.shed_util.load_installed_datatypes( self.app,
tool_shed_repository, relative_install_dir )
File /home/a-m/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py, line
1269, in load_installed_datatypes
work_dir = make_tmp_directory()
File /home/a-m/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py, line
1305, in make_tmp_directory
os.makedirs( work_dir )
File /usr/lib64/python2.6/os.py, line 157, in makedirs
mkdir(name, mode)
OSError: [Errno 17] File exists:
'/home/a-m/galaxy/dist-database/tmp/work_tmp'
Removing PID file web1.pid
--
I was also seeing this using separate runner/webapp ini files and
'run_multiple_processes.sh --daemon', but we decided to go ahead and
migrate over to a unified universe_wsgi.ini file.
Anyway, we found a workaround by rerunning 'GALAXY_RUN_ALL=1 sh run.sh
--daemon' which skips any running services, but I'm curious whether anyone
else has seen this and whether there is a fix (or maybe added config
setting we are missing?)
chris
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[galaxy-dev] Multi-level conditional output files
Hello! The wiki entry on dealing with the filter tags is wonderful, but I seem to hit its limitations, unless someone has experience with multi-level conditionals in the input. For example in my XML, conditional name=Build_Settings param name=SettingsType type=select label=Settings to use option value=preSetUse Defaults/option option value=fullFull parameter list/option /param when value=preSet / when value=full conditional name=Bam param name=Bam_Output type=select label=Bam Output option value=noNo/option option value=yesYes/option /param /conditional /when /conditional The bam conditional sets an argument in my program to generate bam instead of sam (default) which is the reason for the conditional. There are two cases for sam output, when the option is preset, or when full parametersbam_output == no. for this reason It wouldnt work to filter this on the bam_output boolean because it would evaluate to false if preset was chosen. I cannot do a simple change format for the same reason. Do the filter tags only support one boolean check? How would I actually get past the settings parameter and into the bam_output parameter? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Shell script to start Galaxy in multi-server environment
On Aug 8, 2012, at 2:30 PM, Karger, Amir wrote: From: Nate Coraor [mailto:n...@bx.psu.edu] On Aug 2, 2012, at 2:56 PM, Karger, Amir wrote: We're upgrading to a late June Galaxy from a last-year Galaxy. We noticed that the docs say you no longer need 2 different .ini files. Great! Unfortunately, the multiprocess.sh in contrib/ still assumes you have multiple .ini files. multiprocess.sh is out of date, so I've removed it from galaxy-central. run.sh can start and stop all of your processes now, as described at: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application %20Scaling Thanks. Of course, reading some other people's posts and the wiki, it looks like it's not *required* to merge, just recommended. Which means our existing system of running the different scripts on different hosts should continue to work. We figure we can put off the merge thing for a bit. Meanwhile, we're able to restart, and get happy log messages from the jobrunner and two web servers (two servers running on different ports of a Tomcat host). And I can do an upload, which runs locally. But when I try to do a blast, which is supposed to submit to the cluster (and ran just fine on our old install), it hangs and never starts. I would think the database is working OK, since it shows me new history items when I upload and stuff. The web Galaxy log shows that I went to the tool page, and then has a ton of loads to root/history_item_updates, but nothing else. The job handler Galaxy log has nothing since the PID messages when the server started up most recently. A quick search of the archives didn't find anything obvious. (I don't have any obvious words to search for.) Any thoughts about where I should start looking to track this down? Hi Amir, If you aren't setting job_manager and job_handlers in your config, each server will consider itself the manager and handler. If not configured to run jobs, this may result in jobs failing to run. I'd suggest explicitly defining a manager and handlers. --nate Thanks, -Amir ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] a problem with python version
On Aug 8, 2012, at 12:06 PM, Rui Wang wrote: Hi Nate, Thanks for the suggestion. Our cluster does not belong to us so we had to request that to be added by their sysadmin. Before that we modified the code in a few scripts to ignore the deprecation warning, that also fixed the problem, should we remove these mods now since the new pytz is installed? If you upgrade pytz, the DeprecationWarnings should go away, and then you would not need to handle them. A separate question, do you happen to know where I could find the instructions for setting up job submission for PBS/torque? There are pieces and bits information here and there but I didn't see any comprehensive one... Our documentation is at: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster If there's something missing from this, please let us know. Thanks, --nate Best Regards, Rui On Wed, Aug 8, 2012 at 7:54 AM, Nate Coraor n...@bx.psu.edu wrote: On Aug 2, 2012, at 1:59 PM, Rui Wang wrote: Hi All, we are installing a local galaxy instance but we met something puzzling. we are running galaxy on cent os 5.x and python 2.6.1. when we tried to upload data, it failed with the message * Dataset generation errors Dataset 5: brain.fa Tool execution generated the following error message: /usr/usc/python/2.6.1/lib/python2.6/site-packages/pytz/tzinfo.py:5: DeprecationWarning: the sets module is deprecated from sets import Set * However, when we tried to use the galaxy version tied to the OS, which is 2.4.3, we were able to upload successfully. Did anyone have the same experience? Any advice will be greatly appreciated. Hi Rui, I'd suggest upgrading your version of pytz with `easy_install --upgrade pytz`. Newer versions should correctly handle importing sets. --nate Thanks, Rui ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Starting a Cloud Instance
Hi Mark, You can always confirm the zone you started an instance in by logging in to the AWS console and, under Instances, find the instance you're wanting to check. After selecting it, under the instance properties, the zone will be displayed for the given instance. The security group and the key pair are rather important to get right for being able to access the instance. However, it seems you're connecting to an existing cluster and are able to access the web console, so I would think the problem is really in having started the instance in the wrong zone vs. the security key issue? Let us know if you have any more issues, Enis On Wed, Aug 8, 2012 at 9:44 PM, Jennifer Jackson j...@bx.psu.edu wrote: Re-Post to galaxy-dev On 8/7/12 3:01 AM, Mark Lindsay wrote: I wondered if you might be able to help. I have very little computing experience but have been trying to launch a cloud instance for the last 24 hrs. Initially I had problems launching the instance in Sahari i.e. it kept saying that it could not connect to the relevant page. When I have finally got top the CloudMan launch page it is giving the following message [Critical] Volume 'vol-dd6397db' is located in the wrong availability zone for this instance. You MUST terminate this instance and start a new one in zone 'us-east-1a' despite the fact that I am sure I have started in zone 'us-east-1a. How important are the security codes and keys? BW Mark __**_ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/**listinfo/galaxy-devhttp://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org __**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
